6UZV | pdb_00006uzv

The structure of a red shifted photosystem I complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history

Literature

The structure of a red-shifted photosystem I reveals a red site in the core antenna.

Toporik, H.Khmelnitskiy, A.Dobson, Z.Riddle, R.Williams, D.Lin, S.Jankowiak, R.Mazor, Y.

(2020) Nat Commun 11: 5279-5279

  • DOI: https://doi.org/10.1038/s41467-020-18884-w
  • Primary Citation Related Structures: 
    6UZV

  • PubMed Abstract: 

    Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the antenna are important for energy transfer dynamics and yield, however, their precise location remained elusive. Here, we construct a chimeric Photosystem I complex in Synechocystis PCC 6803 that shows enhanced absorption in the red spectral region. We combine Cryo-EM and spectroscopy to determine the structure - function relationship in this red-shifted Photosystem I complex. Determining the structure of this complex reveals the precise architecture of the low energy site as well as large scale structural heterogeneity which is probably universal to all trimeric Photosystem I complexes. Identifying the structural elements that constitute red sites can expand the absorption spectrum of oxygenic photosynthetic and potentially modulate light harvesting efficiency.


  • Organizational Affiliation
    • School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.

Macromolecule Content 

  • Total Structure Weight: 1,086.84 kDa 
  • Atom Count: 72,606 
  • Modeled Residue Count: 6,711 
  • Deposited Residue Count: 6,915 
  • Unique protein chains: 11

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
L [auth a],
M [auth 1]
751Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29254 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
P [auth b],
Q [auth 2]
735Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29255 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC,
N [auth c],
O [auth 3]
81Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P32422 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID,
R [auth d],
S [auth 4]
141Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for P19569 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE,
T [auth e],
U [auth 5]
74Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12975 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIF,
V [auth f],
W [auth 6]
165Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P29256 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I],
X [auth i],
Y [auth h]
40Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q55330 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXAA [auth 7],
H [auth J],
Z [auth j]
40Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q55329 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIDA [auth l],
EA [auth 0],
I [auth L]
157Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P37277 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIFA [auth m],
GA [auth 9],
J [auth M]
31Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P72986 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 2BA [auth k],
CA [auth 8],
K
90Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P74564 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL0

Query on CL0



Download:Ideal Coordinates CCD File
JA [auth A],
PF [auth a],
RH [auth 1]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AB [auth A]
AD [auth B]
AE [auth B]
AF [auth L]
AG [auth a]
AB [auth A],
AD [auth B],
AE [auth B],
AF [auth L],
AG [auth a],
AH [auth a],
AI [auth 1],
AJ [auth 1],
AK [auth b],
AL [auth b],
AM [auth 2],
AN [auth 2],
BB [auth A],
BD [auth B],
BF [auth L],
BG [auth a],
BH [auth a],
BI [auth 1],
BJ [auth 1],
BK [auth b],
BL [auth b],
BM [auth 2],
BN [auth 2],
BP [auth 8],
CB [auth A],
CD [auth B],
CG [auth a],
CH [auth a],
CI [auth 1],
CJ [auth 1],
CK [auth b],
CL [auth b],
CM [auth 2],
CN [auth 2],
CP [auth 8],
DB [auth A],
DD [auth B],
DG [auth a],
DH [auth a],
DI [auth 1],
DJ [auth 1],
DK [auth b],
DL [auth b],
DM [auth 2],
DN [auth 2],
DO [auth 6],
DP [auth 8],
EB [auth A],
ED [auth B],
EG [auth a],
EH [auth a],
EI [auth 1],
EJ [auth 1],
EK [auth b],
EL [auth b],
EM [auth 2],
EN [auth 2],
EO [auth 6],
FB [auth A],
FD [auth B],
FG [auth a],
FI [auth 1],
FJ [auth 1],
FK [auth b],
FL [auth b],
FM [auth 2],
FN [auth 2],
GB [auth A],
GD [auth B],
GG [auth a],
GI [auth 1],
GJ [auth 1],
GK [auth b],
GL [auth b],
GM [auth 2],
GN [auth 2],
HB [auth A],
HD [auth B],
HG [auth a],
HI [auth 1],
HK [auth b],
HL [auth b],
HM [auth 2],
HN [auth 2],
HP [auth l],
IB [auth A],
IC [auth B],
ID [auth B],
IG [auth a],
II [auth 1],
IK [auth b],
IL [auth b],
IM [auth 2],
IN [auth 2],
IP [auth l],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth K],
JG [auth a],
JI [auth 1],
JK [auth b],
JL [auth b],
JM [auth 2],
JN [auth 2],
JP [auth l],
KA [auth A],
KB [auth A],
KD [auth B],
KF [auth K],
KG [auth a],
KI [auth 1],
KK [auth b],
KL [auth b],
KM [auth 2],
KN [auth 2],
KP [auth l],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LF [auth K],
LG [auth a],
LI [auth 1],
LK [auth b],
LM [auth 2],
LN [auth 2],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth F],
MG [auth a],
MI [auth 1],
MK [auth b],
MM [auth 2],
MN [auth 2],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NG [auth a],
NI [auth 1],
NK [auth b],
NM [auth 2],
NO [auth j],
NP [auth 0],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OG [auth a],
OH [auth a],
OI [auth 1],
OK [auth b],
OM [auth 2],
OO [auth j],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth F],
PG [auth a],
PI [auth 1],
PK [auth b],
PM [auth 2],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth F],
QF [auth a],
QG [auth a],
QI [auth 1],
QK [auth b],
QM [auth 2],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RF [auth a],
RG [auth a],
RI [auth 1],
RK [auth b],
RM [auth 2],
RO [auth 7],
RP [auth 0],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SF [auth a],
SG [auth a],
SH [auth 1],
SI [auth 1],
SK [auth b],
SM [auth 2],
SO [auth 7],
SP [auth 0],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TF [auth a],
TG [auth a],
TH [auth 1],
TI [auth 1],
TJ [auth b],
TK [auth b],
TM [auth 2],
TO [auth 7],
TP [auth 0],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth a],
UG [auth a],
UH [auth 1],
UI [auth 1],
UJ [auth b],
UK [auth b],
UM [auth 2],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VE [auth J],
VF [auth a],
VG [auth a],
VH [auth 1],
VI [auth 1],
VK [auth b],
VL [auth 2],
VM [auth 2],
VN [auth f],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WE [auth J],
WF [auth a],
WG [auth a],
WH [auth 1],
WI [auth 1],
WJ [auth b],
WK [auth b],
WM [auth 2],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XF [auth a],
XG [auth a],
XH [auth 1],
XI [auth 1],
XJ [auth b],
XK [auth b],
XL [auth 2],
XM [auth 2],
XO [auth k],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YF [auth a],
YG [auth a],
YH [auth 1],
YI [auth 1],
YJ [auth b],
YK [auth b],
YL [auth 2],
YM [auth 2],
YN [auth f],
YO [auth k],
ZA [auth A],
ZC [auth B],
ZD [auth B],
ZE [auth L],
ZF [auth a],
ZG [auth a],
ZH [auth 1],
ZI [auth 1],
ZJ [auth b],
ZK [auth b],
ZL [auth 2],
ZM [auth 2],
ZN [auth f]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
EF [auth L]
GC [auth A]
GP [auth l]
HC [auth A]
KC [auth B]
EF [auth L],
GC [auth A],
GP [auth l],
HC [auth A],
KC [auth B],
MH [auth a],
MP [auth 0],
NH [auth a],
OJ [auth 1],
OP [auth 0],
VJ [auth b],
WL [auth 2]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
GF [auth M]
HA [auth A]
IA [auth A]
IE [auth B]
NF [auth a]
GF [auth M],
HA [auth A],
IA [auth A],
IE [auth B],
NF [auth a],
OF [auth a],
PH [auth 1],
QH [auth 1],
SL [auth b],
UN [auth 2],
WP [auth m],
XP [auth 9]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AO [auth f]
AP [auth 8]
BC [auth A]
CC [auth A]
CE [auth B]
AO [auth f],
AP [auth 8],
BC [auth A],
CC [auth A],
CE [auth B],
CF [auth L],
CO [auth 6],
DC [auth A],
DE [auth B],
DF [auth L],
EC [auth A],
EE [auth B],
EP [auth 8],
FC [auth A],
FE [auth B],
FO [auth 6],
GE [auth B],
GO [auth 6],
HE [auth B],
HF [auth M],
HH [auth a],
IF [auth K],
IH [auth a],
IO [auth i],
JE [auth B],
JH [auth a],
JJ [auth 1],
JO [auth i],
KH [auth a],
KJ [auth 1],
KO [auth h],
LH [auth a],
LJ [auth 1],
LO [auth h],
LP [auth l],
MF [auth K],
MJ [auth 1],
ML [auth b],
NJ [auth 1],
NL [auth b],
OE [auth F],
OL [auth b],
ON [auth 2],
PL [auth b],
PN [auth 2],
PO [auth j],
PP [auth 0],
QL [auth b],
QN [auth 2],
QO [auth j],
RE [auth F],
RL [auth b],
RN [auth 2],
SE [auth I],
SN [auth 2],
TE [auth I],
TL [auth b],
TN [auth 2],
UL [auth b],
UO [auth 7],
UP [auth 0],
VO [auth 7],
VP [auth 0],
WO [auth k],
XE [auth J],
XN [auth f],
YE [auth J],
YP [auth 9],
ZO [auth k]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
BO [auth 6]
HO [auth i]
MO [auth h]
NE [auth F]
UE [auth I]
BO [auth 6],
HO [auth i],
MO [auth h],
NE [auth F],
UE [auth I],
WN [auth f]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
BE [auth B]
FH [auth a]
HJ [auth 1]
LL [auth b]
NN [auth 2]
BE [auth B],
FH [auth a],
HJ [auth 1],
LL [auth b],
NN [auth 2],
ZB [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AC [auth A]
GH [auth a]
IJ [auth 1]
KE [auth C]
LE [auth C]
AC [auth A],
GH [auth a],
IJ [auth 1],
KE [auth C],
LE [auth C],
PJ [auth c],
QJ [auth c],
RJ [auth 3],
SJ [auth 3]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
FF [auth L],
FP [auth l],
QP [auth 0]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX1.16-3549

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 2.0: 2024-10-30
    Changes: Data collection, Database references, Non-polymer description, Refinement description, Structure summary